Mercurial > repos > imgteam > 2d_histogram_equalization

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planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
author imgteam
date Tue, 23 Jul 2019 14:06:42 -0400
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d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
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diff changeset
1 import argparse
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
2 import os
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
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diff changeset
3 import sys
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
4 import skimage.io
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
5 import skimage.exposure
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
6 import skimage.util
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
7
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
8 hOptions = {
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
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9 'default' : lambda img_raw: skimage.exposure.equalize_hist(img_raw),
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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10 'clahe' : lambda img_raw: skimage.exposure.equalize_adapthist(img_raw)
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
11 }
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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12
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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13 if __name__ == "__main__":
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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14 parser = argparse.ArgumentParser(description='Histogram equalization')
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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15 parser.add_argument('input_file', type=argparse.FileType('r'), default=sys.stdin, help='input file')
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
diff changeset
16 parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file (TIFF)')
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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17 parser.add_argument('h_type', choices=hOptions.keys(), help='histogram equalization method')
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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18 args = parser.parse_args()
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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19
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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20 img_in = skimage.io.imread(args.input_file.name)
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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21 res = hOptions[args.h_type](img_in)
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
parents:
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22 res = skimage.util.img_as_uint(res)
d54f14727f77 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/2d_histogram_equalization/ commit 767d7fec860d01468701c4e6dc270a7f1c74d53c
imgteam
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23 skimage.io.imsave(args.out_file.name, res, plugin="tifffile")